Re: AMBER: Math libraries

From: Robert Duke <>
Date: Thu, 28 Jun 2007 08:15:07 -0400

Francesco -
The MKL helps for generalized Born simulations, but really has no impact on
PME simulations in pmemd, and to my knowledge, also sander. I imagine that
for QM components of amber, there is a benefit in sander, but since pmemd
does none of this stuff, I don't know much about details. I don't doubt
that the acml libraries could be used; others have asked - but it might
require interface code if the code interfaces don't match either MKL or
MASSVP (ibm). Others that know the latest sander stuff can probably comment
further (bottom line - IF you are interested primarily in pme simulations,
don't worry about it..., and IF you are primarily interested in pme
simulations, the best way to go faster is to use pmemd)
Regards - Bob Duke

----- Original Message -----
From: "Francesco Pietra" <>
To: "Amber" <>
Sent: Thursday, June 28, 2007 5:56 AM
Subject: AMBER: Math libraries

> While commanding as user
> $ ./configure -static ifort_x86_64
> for a preliminary serial compilation of amber9, a suggestion arose to set
> MKL_HOME to point to intel's mkl mathematical libraries (which I never
> implemented, being limited to libimf.a and
> On the other hand
> $ ./configure --help
> informs that no great improvement can be expected from mkl libraries. I
> imagine
> the less so for no intel's hardw, such as dual-core-opteron, in my case.
> QUESTION: has anyone tried to compile amber9 with mathematical acml
> libraries
> (from AMD) which are specialized for opteron? Is the advantage so modest
> to
> disregard the issue? At any event, is there any chance to modify the
> Makefile
> to force amber9 to use acml libraries (once installed)?
> Thanks
> francesco pietra
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Received on Sun Jul 01 2007 - 06:07:20 PDT
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